Well, he was captured as a prisoner in Clone Wars volume 1, so I just assumed that he was still under control of the Republic as of ROTS. And after the Republic became the Empire and the Trade Federation was destroyed, he was probably killed.

It says in the novel that he was with the seps on mustafar and when anakin arrived he walked in and carved hit lightsaber through San Hills 3 hearts. Oh, he was also sprung from Republic captivity by the seps.

San Hill was the chairman of the Intergalactic Banking Clan. He was from the planet Muunilinst and of the Muun species. He also was one of the key leaders of the Confederacy of Independent Systems and was present at the first meeting on Geonosis.

The Banking Clan was responsible for supplying hailfire droids to the droid armies of the Confederacy. In addition, San Hill was the primary financier of the rehabilitation of General Grievous, a Kaleesh warlord and CIS general who required extensive cybernetic enhancements in order to be kept alive.

San Hill and the IG Banking Clan were a primary objective of the Battle of Muunilinst, one of the first battles of the Clone Wars, which saw the first war-time appearance of the bounty hunter Durge, the Gen'dai warrior, as well as the IG Lancer droids, predecessors of both the IG-100 MagnaGuards and the Imperial-era bounty hunter IG-88. San Hill was captured by Obi-Wan Kenobi, but later escaped Republic custody.

In the later stages of the Clone Wars, San Hill was hidden on Utapau along with the other members of the Separatist Council by General Grievous as the Confederacy was beginning to lose ground, and they were soon moved to fiery Mustafar. On that volcanic world, Hill was killed Darth Vader.

Though Hill's body is never seen in the film, he is shown to be killed both in the novelization and comic adaptation. Lucasfilm's official stance is that if the events of such adaptations don't explicitly contradict what is seen on the screen, then they can be considered canon. Also, it is unlikely that Hill survived, as he at least would have made an attempt to escape or alert the rest of the Separatist forces; however, it is already known that the galaxy at large, including most of the remaining Separatist army, has no idea what happened on Mustafar.